maser_analysis_foxp1events.Rmd

---
title: "maser visualizing foxp1 event"
author: "Shay Iyer"
date: "`r Sys.Date()`"
output: html_document
editor_options: 
  chunk_output_type: console
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(tidyverse)
library(maser)
library(rtracklayer)
```

```{r}
ips.s1s2.path <- "/Volumes/sheynkman/projects/shay_thesis/input-data/01_ips-s1s2_rmats-out_input"
ips.s1s2 <- maser(path = ips.s1s2.path, cond_labels = c("iPS", "S1S2-iEC"), ftype = "JC")
foxp1.events <- geneEvents(ips.s1s2, geneS = "FOXP1")
plotTranscripts(foxp1.events, event_id = 6043, type = "MXE", gtf = transcript_gtf, zoom = T, show_PSI = TRUE)

plotTranscripts(foxp1.events, event_id = 7984, type = "A3SS", gtf = transcript_gtf, zoom = T, show_PSI = TRUE)
```

```{r}
transcript.gtf.path <- "/Volumes/sheynkman/projects/shay_thesis/input-data/02_long-read-EC-WTC11-1_input/01_annotation/EC_foxp1-enst.gtf"

transcript_gtf <- rtracklayer::import.gff(transcript.gtf.path)


```